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Chlorine in PDB 5wre: Hepatitis B Virus Core Protein Y132A Mutant in Complex with Heteroaryldihydropyrimidine (HAP_R01)

Protein crystallography data

The structure of Hepatitis B Virus Core Protein Y132A Mutant in Complex with Heteroaryldihydropyrimidine (HAP_R01), PDB code: 5wre was solved by Z.Zhou, Z.H.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.20 / 1.95
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 65.241, 66.930, 87.071, 68.28, 69.02, 83.62
R / Rfree (%) 20.7 / 23.9

Other elements in 5wre:

The structure of Hepatitis B Virus Core Protein Y132A Mutant in Complex with Heteroaryldihydropyrimidine (HAP_R01) also contains other interesting chemical elements:

Fluorine (F) 18 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with Heteroaryldihydropyrimidine (HAP_R01) (pdb code 5wre). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 9 binding sites of Chlorine where determined in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with Heteroaryldihydropyrimidine (HAP_R01), PDB code: 5wre:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 5wre

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Chlorine binding site 1 out of 9 in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with Heteroaryldihydropyrimidine (HAP_R01)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Hepatitis B Virus Core Protein Y132A Mutant in Complex with Heteroaryldihydropyrimidine (HAP_R01) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:30.8
occ:1.00
 CL1 A:7TL201 0.0 30.8 1.0
C16 A:7TL201 1.8 33.4 1.0
C11 A:7TL201 2.7 27.8 1.0
C15 A:7TL201 2.7 31.8 1.0
C10 A:7TL201 3.1 31.9 1.0
O02 A:7TL201 3.3 32.2 1.0
CG2 A:ILE105 3.4 29.4 1.0
OG A:SER106 3.6 35.8 1.0
CB A:ILE105 3.7 28.2 1.0
CD1 A:TRP102 3.8 24.2 1.0
C12 A:7TL201 3.9 24.2 1.0
CD2 A:LEU30 4.0 27.6 1.0
C14 A:7TL201 4.0 26.1 1.0
C03 A:7TL201 4.1 35.7 1.0
N09 A:7TL201 4.2 38.3 1.0
C05 A:7TL201 4.2 31.8 1.0
C01 A:7TL201 4.2 30.4 1.0
N A:SER106 4.3 31.8 1.0
NE1 A:TRP102 4.4 30.8 1.0
O A:TRP102 4.4 31.5 1.0
CG2 A:THR33 4.5 24.2 1.0
C13 A:7TL201 4.5 31.8 1.0
CD1 A:ILE105 4.6 19.1 1.0
CA A:TRP102 4.6 25.2 1.0
C A:ILE105 4.6 31.8 1.0
CG A:TRP102 4.6 24.4 1.0
CB A:SER106 4.7 25.8 1.0
CA A:SER106 4.8 31.7 1.0
CG1 A:ILE105 4.8 23.6 1.0
CA A:ILE105 4.8 31.8 1.0
C A:TRP102 5.0 26.8 1.0

Chlorine binding site 2 out of 9 in 5wre

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Chlorine binding site 2 out of 9 in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with Heteroaryldihydropyrimidine (HAP_R01)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Hepatitis B Virus Core Protein Y132A Mutant in Complex with Heteroaryldihydropyrimidine (HAP_R01) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl201

b:30.0
occ:1.00
 CL1 B:7TL201 0.0 30.0 1.0
C16 B:7TL201 1.8 29.8 1.0
C11 B:7TL201 2.7 30.1 1.0
C15 B:7TL201 2.7 32.3 1.0
C10 B:7TL201 3.1 31.4 1.0
O02 B:7TL201 3.3 26.5 1.0
CG2 B:ILE105 3.4 27.2 1.0
OG B:SER106 3.6 37.3 1.0
CB B:ILE105 3.7 22.5 1.0
CD1 B:TRP102 3.8 23.9 1.0
CD2 B:LEU30 4.0 26.6 1.0
C12 B:7TL201 4.0 22.4 1.0
C14 B:7TL201 4.0 32.8 1.0
C01 B:7TL201 4.1 24.2 1.0
N09 B:7TL201 4.1 30.7 1.0
C03 B:7TL201 4.1 24.5 1.0
C05 B:7TL201 4.2 30.7 1.0
N B:SER106 4.4 24.1 1.0
NE1 B:TRP102 4.4 26.9 1.0
O B:TRP102 4.4 27.7 1.0
CD1 B:ILE105 4.5 20.0 1.0
CA B:TRP102 4.5 24.7 1.0
C13 B:7TL201 4.5 30.4 1.0
CG B:TRP102 4.6 27.7 1.0
C B:ILE105 4.6 28.9 1.0
CG2 B:THR33 4.7 21.4 1.0
CG1 B:ILE105 4.7 21.2 1.0
CB B:SER106 4.8 29.0 1.0
CA B:ILE105 4.8 22.4 1.0
CA B:SER106 4.8 23.2 1.0
C B:TRP102 5.0 25.0 1.0
CB B:TRP102 5.0 23.4 1.0

Chlorine binding site 3 out of 9 in 5wre

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Chlorine binding site 3 out of 9 in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with Heteroaryldihydropyrimidine (HAP_R01)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Hepatitis B Virus Core Protein Y132A Mutant in Complex with Heteroaryldihydropyrimidine (HAP_R01) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl202

b:0.7
occ:1.00
 CG B:ARG127 4.7 23.5 1.0
O B:ILE126 5.0 31.7 1.0

Chlorine binding site 4 out of 9 in 5wre

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Chlorine binding site 4 out of 9 in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with Heteroaryldihydropyrimidine (HAP_R01)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Hepatitis B Virus Core Protein Y132A Mutant in Complex with Heteroaryldihydropyrimidine (HAP_R01) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl203

b:73.5
occ:1.00
 NH1 B:ARG39 2.8 70.0 1.0
OE2 B:GLU43 3.4 36.3 1.0
OE1 B:GLU43 3.5 43.3 1.0
O B:HOH350 3.5 69.8 1.0
CB A:ASP2 3.7 38.7 1.0
CD B:GLU43 3.8 46.4 1.0
CZ B:ARG39 3.9 73.8 1.0
N A:ASP2 4.2 41.7 1.0
NH2 B:ARG39 4.3 76.3 1.0
CA A:ASP2 4.6 27.4 1.0
CG A:ASP2 4.8 56.5 1.0
OD2 A:ASP2 4.8 65.3 1.0

Chlorine binding site 5 out of 9 in 5wre

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Chlorine binding site 5 out of 9 in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with Heteroaryldihydropyrimidine (HAP_R01)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Hepatitis B Virus Core Protein Y132A Mutant in Complex with Heteroaryldihydropyrimidine (HAP_R01) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl201

b:30.3
occ:1.00
 CL1 C:7TL201 0.0 30.3 1.0
C16 C:7TL201 1.8 24.7 1.0
C11 C:7TL201 2.7 24.2 1.0
C15 C:7TL201 2.7 31.4 1.0
C10 C:7TL201 3.1 32.3 1.0
O02 C:7TL201 3.4 24.7 1.0
OG C:SER106 3.5 41.7 1.0
CG2 C:ILE105 3.6 29.6 1.0
CD1 C:TRP102 3.7 22.9 1.0
CB C:ILE105 3.8 27.4 1.0
CD2 C:LEU30 3.8 32.5 1.0
C12 C:7TL201 4.0 23.5 1.0
C14 C:7TL201 4.0 28.5 1.0
C01 C:7TL201 4.1 24.0 1.0
N09 C:7TL201 4.1 36.7 1.0
C03 C:7TL201 4.2 32.4 1.0
C05 C:7TL201 4.2 35.2 1.0
O C:TRP102 4.3 29.6 1.0
NE1 C:TRP102 4.3 25.8 1.0
N C:SER106 4.4 25.9 1.0
CA C:TRP102 4.4 23.4 1.0
CD1 C:ILE105 4.5 27.7 1.0
CG C:TRP102 4.5 24.4 1.0
C13 C:7TL201 4.5 31.5 1.0
CG2 C:THR33 4.6 32.7 1.0
C C:ILE105 4.6 33.2 1.0
CG1 C:ILE105 4.7 28.5 1.0
CB C:SER106 4.7 30.9 1.0
CA C:SER106 4.8 29.0 1.0
CA C:ILE105 4.8 30.4 1.0
CB C:TRP102 4.9 20.1 1.0
C C:TRP102 4.9 29.0 1.0

Chlorine binding site 6 out of 9 in 5wre

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Chlorine binding site 6 out of 9 in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with Heteroaryldihydropyrimidine (HAP_R01)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Hepatitis B Virus Core Protein Y132A Mutant in Complex with Heteroaryldihydropyrimidine (HAP_R01) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl201

b:31.1
occ:1.00
 CL1 D:7TL201 0.0 31.1 1.0
C16 D:7TL201 1.8 20.0 1.0
C11 D:7TL201 2.7 22.3 1.0
C15 D:7TL201 2.7 28.4 1.0
C10 D:7TL201 3.2 28.3 1.0
O02 D:7TL201 3.3 28.6 1.0
CG2 D:ILE105 3.4 20.1 1.0
OG D:SER106 3.6 37.2 1.0
CD1 D:TRP102 3.7 23.3 1.0
CB D:ILE105 3.8 23.4 1.0
CD2 D:LEU30 3.9 28.7 1.0
C12 D:7TL201 4.0 19.1 1.0
C14 D:7TL201 4.0 29.5 1.0
C03 D:7TL201 4.1 35.6 1.0
C01 D:7TL201 4.2 29.5 1.0
C05 D:7TL201 4.2 27.6 1.0
N09 D:7TL201 4.2 42.5 1.0
NE1 D:TRP102 4.3 23.8 1.0
N D:SER106 4.4 22.5 1.0
O D:TRP102 4.4 30.3 1.0
CG2 D:THR33 4.5 22.2 0.8
CA D:TRP102 4.5 19.7 1.0
C13 D:7TL201 4.5 28.4 1.0
CG D:TRP102 4.5 25.2 1.0
CD1 D:ILE105 4.6 26.2 1.0
OG1 D:THR33 4.6 24.8 0.1
C D:ILE105 4.6 32.1 1.0
CB D:SER106 4.8 30.8 1.0
CG1 D:ILE105 4.8 24.8 1.0
CA D:SER106 4.8 25.2 1.0
CA D:ILE105 4.8 30.6 1.0
CB D:TRP102 4.9 20.7 1.0
C D:TRP102 5.0 23.7 1.0

Chlorine binding site 7 out of 9 in 5wre

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Chlorine binding site 7 out of 9 in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with Heteroaryldihydropyrimidine (HAP_R01)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Hepatitis B Virus Core Protein Y132A Mutant in Complex with Heteroaryldihydropyrimidine (HAP_R01) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl203

b:79.8
occ:1.00
 O D:HOH390 2.4 76.2 1.0
O D:HOH345 2.7 40.4 1.0
O D:HOH308 3.3 33.7 1.0
O C:HOH366 4.0 55.6 1.0
OD2 D:ASP2 4.2 75.5 1.0
NZ D:LYS7 4.3 49.4 1.0
O D:HOH374 4.3 62.7 1.0
O D:HOH344 4.5 41.7 1.0
CD D:LYS7 4.5 45.4 1.0
CB D:ASP4 4.6 30.8 1.0
O D:ASP2 4.7 41.0 1.0
CG D:ASP2 4.7 62.9 1.0
O D:HOH332 4.8 28.2 1.0
CE D:LYS7 4.9 41.0 1.0

Chlorine binding site 8 out of 9 in 5wre

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Chlorine binding site 8 out of 9 in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with Heteroaryldihydropyrimidine (HAP_R01)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Hepatitis B Virus Core Protein Y132A Mutant in Complex with Heteroaryldihydropyrimidine (HAP_R01) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl201

b:30.4
occ:1.00
 CL1 E:7TL201 0.0 30.4 1.0
C16 E:7TL201 1.8 33.5 1.0
C11 E:7TL201 2.7 31.9 1.0
C15 E:7TL201 2.8 35.2 1.0
C10 E:7TL201 3.1 36.5 1.0
O02 E:7TL201 3.3 33.2 1.0
OG E:SER106 3.5 35.3 1.0
CG2 E:ILE105 3.5 32.6 1.0
CD1 E:TRP102 3.7 26.8 1.0
CB E:ILE105 3.8 28.8 1.0
CD2 E:LEU30 3.9 27.3 1.0
C12 E:7TL201 4.0 22.7 1.0
C14 E:7TL201 4.0 37.3 1.0
N09 E:7TL201 4.1 30.6 1.0
C01 E:7TL201 4.1 35.3 1.0
C03 E:7TL201 4.1 33.9 1.0
C05 E:7TL201 4.1 35.0 1.0
NE1 E:TRP102 4.3 31.1 1.0
N E:SER106 4.3 35.8 1.0
O E:TRP102 4.4 29.7 1.0
CA E:TRP102 4.5 23.7 1.0
CG E:TRP102 4.5 24.5 1.0
C13 E:7TL201 4.6 31.0 1.0
CG2 E:THR33 4.6 26.8 1.0
C E:ILE105 4.6 31.9 1.0
CD1 E:ILE105 4.6 26.9 1.0
CB E:SER106 4.7 30.8 1.0
CA E:SER106 4.7 30.1 1.0
CG1 E:ILE105 4.8 28.9 1.0
CA E:ILE105 4.8 25.1 1.0
C E:TRP102 4.9 29.2 1.0
CB E:TRP102 5.0 20.9 1.0

Chlorine binding site 9 out of 9 in 5wre

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Chlorine binding site 9 out of 9 in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with Heteroaryldihydropyrimidine (HAP_R01)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Hepatitis B Virus Core Protein Y132A Mutant in Complex with Heteroaryldihydropyrimidine (HAP_R01) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl201

b:30.5
occ:1.00
 CL1 F:7TL201 0.0 30.5 1.0
C16 F:7TL201 1.8 33.4 1.0
C11 F:7TL201 2.7 30.9 1.0
C15 F:7TL201 2.8 36.6 1.0
C10 F:7TL201 3.1 37.7 1.0
O02 F:7TL201 3.3 29.0 1.0
CG2 F:ILE105 3.4 26.9 1.0
OG F:SER106 3.5 42.0 1.0
CB F:ILE105 3.6 25.8 1.0
CD1 F:TRP102 3.8 29.6 1.0
C12 F:7TL201 4.0 23.2 1.0
C14 F:7TL201 4.1 34.9 1.0
CD2 F:LEU30 4.1 29.5 1.0
N09 F:7TL201 4.2 35.5 1.0
C03 F:7TL201 4.2 30.3 1.0
C05 F:7TL201 4.2 31.3 1.0
C01 F:7TL201 4.2 28.2 1.0
N F:SER106 4.3 29.0 1.0
NE1 F:TRP102 4.3 38.4 1.0
O F:TRP102 4.3 36.1 1.0
CD1 F:ILE105 4.5 31.7 1.0
C F:ILE105 4.5 30.0 1.0
CG2 F:THR33 4.5 27.2 1.0
CA F:TRP102 4.5 26.7 1.0
CG F:TRP102 4.6 27.5 1.0
C13 F:7TL201 4.6 28.7 1.0
CB F:SER106 4.6 31.4 1.0
CA F:SER106 4.7 27.3 1.0
CG1 F:ILE105 4.7 27.1 1.0
CA F:ILE105 4.7 31.9 1.0
C F:TRP102 4.9 27.2 1.0
CB F:TRP102 5.0 23.5 1.0

Reference:

Z.Zhou, T.Hu, X.Zhou, S.Wildum, F.Garcia-Alcalde, Z.H.Xu, D.Wu, Y.Mao, X.Tian, Y.Zhou, F.Shen, Z.Zhang, G.Tang, I.Najera, G.Yang, H.C.Shen, J.A.T.Young, N.Qin. Heteroaryldihydropyrimidine (Hap) and Sulfamoylbenzamide (Sba) Inhibit Hepatitis B Virus Replication By Different Molecular Mechanisms Sci Rep V. 7 42374 2017.
ISSN: ESSN 2045-2322
DOI: 10.1038/SREP42374
Page generated: Fri Jul 26 20:39:30 2024

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